main.yml

name: Update Dependabot PR

on:
  pull_request_target:
    types: [opened, reopened, synchronize]

permissions:
  contents: write
  pull-requests: write

jobs:
  update_config:
    if: github.actor == 'dependabot[bot]'
    runs-on: ubuntu-latest
    steps:
      - name: Checkout PR branch
        uses: actions/checkout@v4
        with:
          # This specifically checks out the PR's branch, not the base branch
          ref: ${{ github.event.pull_request.head.ref }}
          token: ${{ secrets.PAT }}

      - name: Parse Docker image and update Nextflow config
        run: |
          # Define file paths
          DOCKERFILE="Dockerfile"
          CONFIG_FILE="nextflow.config"

          # Use grep and awk to extract the full image name and tag
          FULL_IMAGE=$(grep -m 1 '^FROM' $DOCKERFILE | awk '{print $2}')

          if [ -z "$FULL_IMAGE" ]; then
            echo "Error: Could not find 'FROM' line in Dockerfile."
            exit 1
          fi

          # Separate the image base name from the version tag
          IMAGE_BASE=$(echo $FULL_IMAGE | cut -d: -f1)
          NEW_VERSION=$(echo $FULL_IMAGE | cut -d: -f2)

          echo "Found Docker image: $IMAGE_BASE"
          echo "Found new version: $NEW_VERSION"

          # Use sed to find the specific container line by its base name and update the version
          sed -i "s|container = '$IMAGE_BASE:.*'|container = '$IMAGE_BASE:$NEW_VERSION'|g" $CONFIG_FILE

          echo "Successfully updated $CONFIG_FILE with image: $IMAGE_BASE:$NEW_VERSION"

      - name: Create commit and push changes
        run: |
          git config --global user.name 'github-actions[bot]'
          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
          git add nextflow.config
          # Check if there are changes to commit to avoid an error
          if ! git diff-index --quiet HEAD; then
            git commit -m "chore: Update container version from Dockerfile"
            git push
          else
            echo "No changes to commit."
          fi